The hyporheic zone is of great interest for stream ecologists because of its role in stream biogeochemical processing. Our study addresses the effects of leaf-litter inputs and varying discharge on surface–hyporheic water exchange and their possible consequences for the hyporheic zone biogeochemistry. Our study was conducted during autumn in Riera de Santa Fe (northeastern Iberian Peninsula), a stream with a well developed deciduous riparian canopy. We placed 15 wells spaced at 5-m intervals longitudinally down the study reach and measured surface and hyporheic nutrient and dissolved O2 (DO) concentrations on 23 sampling dates (15 during the leaffall period and 8 after a flood that washed out 65% of the accumulated leaf biomass). We assessed changes in surface-water exchange and in hyporheic NH4-N and soluble reactive P (SRP) uptake via coinjection of a conservative tracer and nutrients. Compared to surface water, hyporheic water had lower DO, higher SRP and NO3-N concentrations, and similar NH4-N concentration. Hyporheic water had higher DO saturation (p = 0.00) and higher NH4-N concentration (p = 0.00) in downwelling than in upwelling wells, whereas SRP and NO3-N concentrations did not differ significantly between well types (p > 0.05). Hydrologic connectivity was higher in downwelling than in upwelling wells and decreased with leaf-litter accumulation in the stream channel and increased with stream discharge. Increased connectivity after a flood reduced the difference in DO between surface and hyporheic compartments in upwelling and downwelling wells and in NO3-N in upwelling wells. NH4-N and SRP uptake responded differently to these changes. Hyporheic SRP uptake rate was controlled by hyporheic SRP concentration, which did not vary with changes in connectivity, whereas NH4-N uptake rate was indirectly affected by changes in connectivity through the influence of connectivity on DO availability. Last, although no NO3-N was added during the solute injections, we observed an increase in hyporheic NO3-N that probably was caused by nitrification. Together these results illustrate how the combination of stream hydrology and organic matter accumulation can dictate seasonal changes in hyporheic biogeochemistry.